NM_001136193.2(FASTKD2):c.823A>G (p.Thr275Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001986013.4

Allele description [Variation Report for NM_001136193.2(FASTKD2):c.823A>G (p.Thr275Ala)]

NM_001136193.2(FASTKD2):c.823A>G (p.Thr275Ala)

Genes:

LOC126806484:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:207634423-207635622 [Gene]
FASTKD2:FAST kinase domains 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q33.3

Genomic location:

Preferred name:

NM_001136193.2(FASTKD2):c.823A>G (p.Thr275Ala)

HGVS:

NC_000002.12:g.206770136A>G
NG_008984.1:g.9749A>G
NM_001136193.2:c.823A>GMANE SELECT
NM_001136194.2:c.823A>G
NM_014929.4:c.823A>G
NP_001129665.1:p.Thr275Ala
NP_001129666.1:p.Thr275Ala
NP_055744.2:p.Thr275Ala
NC_000002.11:g.207634860A>G

Protein change:

T275A

Links:

dbSNP: rs200827808

NCBI 1000 Genomes Browser:

rs200827808

Molecular consequence:

NM_001136193.2:c.823A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001136194.2:c.823A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014929.4:c.823A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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spliceosome associated protein 114 (SF3a) [Homo sapiens]
spliceosome associated protein 114 (SF3a) [Homo sapiens]
gi|3212998|gb|AAC23435.1||gnl|WUGSC 130H16.3

Protein
match to ESTs Z43979 (NID:g573097), R19699 (NID:g774333), and C01164 (NID:g14333...
match to ESTs Z43979 (NID:g573097), R19699 (NID:g774333), and C01164 (NID:g1433394); alternatively spliced form of H_DJ130H16.1a (C-terminal truncation confirmed by C01164) [Homo sapiens]
gi|3212995|gb|AAC23432.1||gnl|WUGSC 130H16.1b

Protein
alpha amylase [Frankliniella occidentalis]
alpha amylase [Frankliniella occidentalis]
gi|2837695838|gb|XIJ67916.1|

Protein
cytochrome oxidase subunit 1, partial (mitochondrion) [Thripidae sp. BOLD:ACI270...
cytochrome oxidase subunit 1, partial (mitochondrion) [Thripidae sp. BOLD:ACI2703]
gi|1002628461|gb|AMN05755.1|

Protein
Echinothrips americanus genes for 5.8S rRNA, ITS2, 28S rRNA, partial and complet...
Echinothrips americanus genes for 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence, specimen_voucher: NCHU:Tai750-2
gi|849389005|dbj|AB972992.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002260489	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002260489

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002260489.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The alanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1480681). This variant has not been reported in the literature in individuals affected with FASTKD2-related conditions. This variant is present in population databases (rs200827808, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 275 of the FASTKD2 protein (p.Thr275Ala).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine